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Viral Pathogen Detection Sars Cov 2 App Note
Viral Pathogen Detection Sars Cov 2 App Note
In this application note, we show: Multiplexed qPCR solutions have been developed that
screen for small numbers of relevant pathogens (for
• Strategies for designing fragment analysis–based target
example, see Ramanan et al. [1]). Nevertheless, the
multiplexing solutions
relatively small capacity of multiplexed qPCR reactions can
• How fragment analysis by capillary electrophoresis (CE) limit throughput when large numbers of target sequences
can provide a sensitive method for detecting pathogens or pathogens need to be detected. A rapid, simple, and
sensitive method is needed in which multiple targets can
• A simple method for detecting SARS-CoV-2 be processed and analyzed at the same time.
viral sequences
Fragment analysis by CE provides an attractive method
Introduction for rapid analysis of multiple targets (Figure 1A). For target
Infectious diseases can present significant global problems. multiplexing, PCR amplicons can be designed such that
The recent SARS-CoV-2 crisis has disrupted economic the length and 5´-terminal fluorophore of the amplicon are
and personal activities, and continues to pose a serious unique to a given target. A single PCR reaction can be set
risk to certain populations, including the elderly and those up with a pool of fluorescently labeled primer sets, and the
with underlying conditions. It is therefore critical to rapidly resulting differently sized PCR fragments can be separated
study individuals who might be infected so that appropriate and detected by CE. High resolution of target fragment
control and containment procedures can be determined. lengths is achieved in CE by running a size standard in the
same injection, ensuring confidence in results.
A wide variety of genetic analysis techniques can be
used to detect pathogenic organisms, including viruses. Here we describe a simple workflow in which multiple
Next-generation sequencing (NGS) is ideal for discovering amplicons from a pathogenic virus can be analyzed using
new organisms and new variants of known strains. fragment analysis (Figure 1B). To illustrate this approach,
However, NGS technologies require sophisticated sample we analyze targets derived from SARS-CoV-2. We show
preparation and data analysis protocols. As a result, they how positive-control synthetic DNA sequences can be
are more suited for discovery and epidemiological studies. used to define and resolve the fragment sizes of the target
On the other hand, quantitative real-time PCR (qPCR) amplicons. We illustrate the sensitivity of the method using
methods utilize simplified workflows that yield clear results known quantities of the SARS-CoV-2 RNA genome. For
when identity of the pathogens needs to be confirmed. details on the protocol, see “Detection of RNA from
SARS-CoV-2 using fragment analysis” [2].
A * * *
orf1-ab Spike (S) Nucleocapsid (N)
*
* PCR
*
Capillary electrophoresis
*
Primer Sample
pool
B Capillary
Collect sample Extract RNA PCR Analyze results
electrophoresis
Figure 1. Workflow for a fragment analysis–based pathogen detection solution. (A) Primers are designed to target regions of pathogens and a
spike-in control (e.g., Applied Biosystems™ VetMAX™ Xeno™ Internal Positive Control (IPC) RNA). As an example, we show the primer pairs for SARS-
CoV-2. For each primer pair, the forward primer is labeled with a fluorophore (*). The primers are pooled and mixed with a sample, which is then amplified
and analyzed by capillary electrophoresis. The targets are distinguished by the different sizes of the amplicons. (B) Thermo Fisher Scientific has all the
tools needed to perform the analysis. Once the sample is collected, data can be obtained in as little as 2 hours.
Description of method
The analysis of multiple amplicons using CE-based Here we illustrate this method using SARS-CoV-2 as
fragment analysis is a widely used strategy in many an example. For redundancy, we designed primers that
different applications, from human identification to research target three different regions of the viral genome: the
on infectious and inherited diseases to oncology research. nucleocapsid protein (N) gene, the spike protein (S) gene,
Briefly, for this application, after identifying suitable and orf1-ab. Examples of the primers that were used in
target sequences, amplicons should be designed to be this study to amplify SARS-CoV-2 sequences are shown in
150–500 nucleotides long. Each amplicon should have a Figure 2. For development of the method, we synthesized
unique length, differing from other amplicons by at least 5 the target amplicons (see ref. 2). In addition, we obtained
nucleotides. The forward primer should be labeled at the purified viral RNA from commercial sources (BEI). As a
5´ end with the fluorescent dye, and the reverse primer control for cDNA synthesis and detection, we used the
should be unlabeled. Reverse transcription polymerase VetMAX Xeno IPC RNA. RT-PCR was performed using
chain reactions (RT-PCR) are then set up using a system samples with viral nucleic acid sequences mixed with the
that allows for cDNA synthesis followed by endpoint PCR pool of primers (final concentration 80 pM each), TaqMan
in a single tube (e.g., Applied Biosystems™ TaqMan® Fast Fast Virus 1-Step Master Mix, 0.5 µL VetMAX Xeno IPC
Virus 1-Step Master Mix). The nucleic acid samples are RNA, and 1 ng human genomic DNA (optional to help
subjected to PCR and the resulting fragments separated prevent stochastic loss of small amounts of target) in a
by CE. The appearance or absence of pathogen-specific 10 µL reaction. Amplicons were generated on either an
fragments of the expected sizes determines the presence Applied Biosystems™ Veriti™ Fast or ProFlex™ thermal cycler
or absence of the pathogen in the sample (Table 1). The and analyzed on either a SeqStudio™ or 3500 Genetic
height of the peaks can be a semi-quantitative indicator of Analyzer. Results were analyzed using Applied Biosystems™
the abundance of the targets in a sample. The principles GeneMapper™ Software. For more details on the method,
and applications of fluorescent DNA fragment analysis see ref. 2.
using high-resolution CE are explained in our Fragment
Analysis User Guide [3]. Primer name Sequence
Figure 3. Electropherogram traces of analysis of SARS-CoV-2 target concentrations. (A) Synthetic DNA targets corresponding to the nucleocapsid
protein (N), spike protein (S), and orf1-ab genes, along with a spiked-in VetMAX Xeno RNA control, were amplified using fluorescent primers and
separated by capillary electrophoresis. Note the clear size separation of the chosen sequences and the presence of the amplicon from the VetMAX Xeno
RNA control in the same capillary. The numbers in the boxes indicate the measured size of the peak in nucleotides. (B) Viral RNA analyzed at 50 copies/
reaction. Note that the amplicon of the N gene transcript is the most abundant, followed by those of orf1-ab and the S gene transcript. The y-axis was
magnified to focus on the SARS-CoV-2 peaks.
In silico inclusivity/exclusivity
To help ensure optimal performance of an assay, candidate high homology with other pathogens, while the forward
primer sequences should be chosen to maximize detection primer for the N gene had high homology with other
of target organisms/strains and minimize detection of coronavirus sequences. Importantly, because there was
off-target sequences. Typically, this is done by performing no homology with the corresponding reverse primer, no
a BLAST search of candidate primer sequences against off-target amplification product would be expected. In other
sequences deposited in databases. To illustrate an cases, there was lower homology for both primers of a
example, we performed a BLAST search of the NCBI pair. However, the PCR annealing conditions are such that
Genbank viral database and complete bacterial and fungal any homologies less than 80% should not bind, so no off-
genome database using the forward and reverse primers target amplification product would be expected. And even
for SARS-CoV-2. Some of the sequence homologies are if the organism was present and anomalous priming did
shown in Table 2. For simplicity, we show only a portion of occur, it is highly unlikely that the 425 nt amplicon would be
all the results returned but illustrate the highest homologies produced by the orf1-ab primers.
that were detected. Two of the reverse primers showed
Table 2. In silico analysis of potential cross-reactivity with other pathogens. Results of a BLAST search of the NCBI Genbank viral database and
complete genomes of selected bacteria and fungi using the primers designed for SARS-CoV-2. Only the highest homologies are shown. Note that
although some primers have >80% homology, the partner primer is either not homologous or has low enough homology to be predicted to not bind in the
PCR reaction. FP = forward primer, RP = reverse primer.
Genbank
Organism Strain Assay % Homology test FP % Homology test RP
accession No.
Bat coronavirus 16B0133 KY938558.1 Nprot_r 95 0
Bat SARS coronavirus HKU3-1 HKU3-1 DQ022305.2 Nprot_r 95 0
Bat SARS coronavirus HKU3-12 HKU3-12 GQ153547.1 Nprot_r 95 0
Bat SARS coronavirus HKU3-2 NA DQ084199.1 Nprot_r 95 0
Bat SARS coronavirus HKU3-3 NA DQ084200.1 Nprot_r 95 0
Figure 4. Cross-reactivity with other pathogens. (A) List of organisms in ZeptoMetrix™ NATtrol™ respiratory pathogen panel pools and individual
NATtrol preparations (SARS and MERS) analyzed using the SARS-CoV-2 sequences described above. No positive calls were made on organisms in any of
the pools or individual preparations. (B) Representative electropherogram traces of analysis of RNA purified from MERS (top), SARS-CoV-2 (middle), and
no-template control (bottom) samples.
Limit of detection pathogen is present or absent in a sample. To illustrate
Establishing the limit of detection (LOD) is an important way how to determine the dynamic range of a fragment
to evaluate performance of an assay. Although this can analysis–based method, we made a dilution series
be defined in many ways, a commonly used metric is to of 12 replicate concentrations of SARS-CoV-2, from
define the concentration for which a true positive detection 2 x 106 copies/reaction to 2 copies/reaction. To get an
can be made in at least 95% of samples. A straightforward approximation of the abundance of targets, we measured
way to determine the LOD is to analyze serial dilutions of the peak heights of the target amplicons at each
the sample to find an approximate LOD, then verify that concentration (Figure 5A). Note that for the concentration
concentration with multiple replicates of concentrations range between 2 and 2 x 103 copies/reaction, there is a
above and below that approximation. For example, initial strong correlation between the input copy number and
experiments using SARS-CoV-2 viral RNA genomes peak height (R2 averaged 0.96). For input amounts higher
suggested we could detect around 5–10 copies per than 2 x 103 copies/reaction, however, the fluorescence
reaction. To verify that result, we set up technical replicates detector became saturated, and signal level measured
of 24 reactions, using 0, 2, 5, and 10 copies/reaction was not correlated with the number of copies present.
(Table 3). These results demonstrated that we could detect Nevertheless, it was clear that viral target sequences
10 viral RNA genome copies in ~95% of the reactions. were present in those samples and they could therefore
Although it was possible to detect 2 and 5 copies in some be scored positive based on the criteria described above
of the samples, other samples in the same concentration (Figure 5B).
range were indeterminate or negative. This dropped the
percentage that scored positive below the 95% threshold. A
Thus, even though the assay may be capable of detecting
2–5 copies/reaction, 10 copies/reaction is achievable 95%
of the time and is therefore an accurate measurement of
the LOD for this assay. Of course, other pathogens and
primer sets may produce different results; therefore it is Xeno
necessary to determine LOD for the specific assay system N
orf1-ab
that will be used. S
Dynamic range Figure 5. Dynamic range of assay that uses SARS-CoV-2 primers.
(A) Plot of peak height versus copy number. Above 2,000 copies/
Another consideration in designing a pathogen detection reaction, the detector measures positive signal but is not quantitative. At
test is the target concentration range at which a positive 2,000 copies and below, there is a strong correlation between peak height
signal can be detected. This could be determined and copy number. Regression (red line on graph) can define a relationship
of y = axb, where y = peak height, x = input copy number, and a and b are
in one of two ways, depending on the needs of the amplicon-specific constants. Overall, the correlation average R2 is 0.96
assay. One way is to determine the concentrations at for all SARS-CoV-2 peaks. Note that the blue markers are the VetMAX
which a positive signal can be quantifiably detected. Xeno RNA control, spiked in at a constant concentration across all input
ranges. (B) Using the criteria described in Table 1, positive samples can be
However, in pathogen detection research assays, it is detected over at least 6 orders of magnitude of input.
not always necessary to determine exact quantities of
the pathogen; it may be sufficient to know whether the
If a quantitative determination for highly concentrated VetMAX Xeno RNA:N gene:orf1-ab:S gene. The reverse
samples is required, there are several options. The easiest primer concentrations were not altered in either mix. In
method is to dilute the samples in a buffer such as TE and a sample containing 2 x 104 copies of RNA targets, the
repeat the assay. If the peak height of the diluted sample unattenuated primer set produced detector saturation of
falls within the previously determined quantitative range, all peaks (Figure 6). However, the same concentration of
then the approximate copy number in the undiluted sample targets analyzed by the attenuated primer set had VetMAX
can be determined. Another method is to attenuate peak Xeno RNA control and N gene peaks reduced to below
heights by limiting the amount of primers. For example, saturation, while leaving the orf1-ab and S gene peaks
one of the highest-expressed targets during SARS-CoV-2 unaffected. Thus, primer attenuation may be an effective
infection is the gene encoding the nucleocapsid protein strategy for analyzing highly concentrated samples.
(N) [4]. This can be seen in the peak heights relative to However, doing so may affect the LOD, since low levels
orf1-ab and the spike protein (S) gene in SARS-CoV-2 of target may not get amplified using attenuated primers.
viral RNA preps (Figure 3). To attenuate the N gene signal, Determining whether or not to use attenuated primers will
we made a primer mix where the concentrations of the therefore depend on the relative concentrations of targets
N gene and VetMAX Xeno RNA fluorescent primers and will require balancing the need for sensitivity vs.
were reduced, for a concentration ratio of 0.3:0.3:1:1 for high-concentration quantification.
Figure 6. Primer attenuation can reduce very high signals. 20,000 copies of SARS-CoV-2 RNA targets were analyzed using either (top) unattenuated
primers (1:1:1:1 ratio of fluorescent forward primers for VetMAX Xeno RNA control, N gene, orf1-ab, and S gene) or (bottom) attenuated primers
(0.3:0.3:1:1). Note that when unattenuated primers were used, all the peaks were saturated (pink lines). However, attenuating the primers for the VetMAX
Xeno RNA and N gene reduced their amplicons’ overall signal to below saturation, while not affecting the other two peaks. This strategy may be used to
reduce signals from samples that have very high concentrations of target sequences.
Summary References
In this application note, we have outlined a general strategy 1. Ramanan P et al. (2017) Syndromic Panel-based Testing in Clinical Microbiology.
Clin Microbiol Rev 15:31(1):e00024-17. doi:10.1128/CMR.00024-17.
for designing a multiplexed target fragment analysis 2. Detection of RNA from SARS-CoV-2 using fragment analysis. https://assets.
solution for detecting pathogenic sequences. We suggest thermofisher.com/TFS-Assets/GSD/Scientific%C2%A0Guides/detection-
designing amplicons for target sequences that are between sarscov2-fragment-analysis-protocol.pdf
3. DNA fragment analysis by capillary electrophoresis. https://www.thermofisher.com/
150 and 500 nucleotides long and including a process us/en/home/life-science/sequencing/fragment-analysis.html
control target that can be spiked into reactions at the 4. Kim D et al. (2020) The architecture of SARS-CoV-2 transcriptome. Cell 181:914-921.
beginning of the protocol and analyzed along with the https://doi.org/10.1016/j.cell.2020.04.011.
specific targets. We suggest performing in silico analyses
to characterize the potential cross-reactivity with other
pathogens and strains that will be covered by the assay.
We illustrate how the LOD and dynamic range may be
analyzed and adjusted, if needed. Finally, we show how
all these suggestions can be implemented by defining
a protocol that may be used to detect SARS-CoV-2
sequences in research samples. In general, a fragment
analysis–based, multiplexed target approach using CE
gives investigators another tool for analyzing the presence
of genomic sequences of pathogenic organisms using a
method that is rapid, simple, and sensitive.
Ordering information
Product Quantity Cat. No.
MagMAX Viral/Pathogen Nucleic Acid Isolation Kit 1 kit A42352
TaqMan Fast Virus 1-Step Master Mix 1 mL 4444432
MicroAmp Clear Adhesive Film 100 films 4306311
5´-labeled/unlabeled primer pairs 10 nmol 450056
VetMAX Xeno Internal Positive Control RNA 100 reactions A29763
Veriti 96-Well Fast Thermal Cycler 1 instrument 4375305
Hi-Di Formamide 25 mL 4311320
DS-33 Matrix Standard Kit (Dye Set G5) 8 runs 4345833
GeneScan 600 LIZ Dye Size Standard v2.0 800 reactions 4408399
SeqStudio Genetic Analyzer 1 system A35644
3500 Genetic Analyzer for Fragment Analysis 1 system A30468
GeneMapper Software 6, full installation 1 license 4475073